Re: ABF simulations

From: Sébastien Légaré (
Date: Tue Jun 23 2009 - 11:01:22 CDT

Dear Sumanth and NAMD users

I do not have a final answer to this question but we have had the same
problem. In most cases, we used a distance reaction coordinate between two
amino acids in a protein. Since the amino acids are constrained by the rest
of the protein and do not sample a larger volume at larger distances, I
suspected that the problem came from a too large Jacobian correction term. If
you used the zCoord reaction coordinate there is no Jacobian term and I still
do not see why this happens. You can try setting forceConst to 100
kcal/mol/Angstroms^2 as suggested in page 3 of Chipot, Hénin, J. Chem. Phys.
123, 244906 (2005).

Sébastien Légaré

On June 9, 2009 10:08:10 pm Sumanth Jamadagni wrote:
> Dear NAMD users,
> We have been trying to run some simple ABF simulations to calculate to
> PMF along z between a molecule and a surface (or similar systems, we
> have faced the same problem).
> The problem is this: we specify an /ximax/ and /ximin/ for the reaction
> coordinate. The center of mass of the molecule initially samples the
> reaction cordinate and then the molecule is stuck at one end of the
> reaction coordinate (ximax or ximin) and doesn't diffuse and sample the
> whole range any more. It therefore accumulates statistics only in the
> first or last few bins, and there are very few statistics in the rest of
> the bins. I will try running the sims for much longer to see if that
> helps, but I suspect I am missing something.
> Thanks
> Sumanth Jamadagni

Sébastien Légaré
Ph. D. Student
Laval University
Quebec, Canada, G1V 0A6
418-656-2131 #11577

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:56 CST